The rete testis and subcapsular compartment of the testis are sites of disease onset in murine experimental auto-immune orchitis, but macrophages in these compartments are not well-characterised. Macrophages were localised by immunohistochemistry using an anti-F4/80 antibody in testis from adult wild-type mice (n=10-17) and mice with a GFP-expressing transgene at the locus of the macrophage receptor, CX3CR1 (Cx3cr1gfp/+;n=6). Sections were also co-labelled by immunofluorescence for the anti-inflammatory marker, CD206, and the antigen-presenting MHC class II molecule (I-A/1-E) to identify activated macrophages. Sections were scanned (Olympus VS120 slide-scanner), measured (Fiji) and macrophages were enumerated (1-3 sections/animal) using stereological techniques. Compared with parenchyma surrounding the seminiferous tubules, volume density of interstitial macrophages (30 macrophages/µm3) was 10-fold higher in the rete testis, and the density of peritubular macrophages (3.5 macrophages/µm3) was 3-fold higher. Macrophage density in subcapsular region was similar to the rest of the parenchyma, and macrophages were also observed within the tunica albuginea itself. In contrast to interstitial macrophages between seminiferous tubules, which lack MHCII expression, most interstitial macrophages in the rete testis and subcapsular region were CX3CR1+F4/80+MHCIIhigh. Peritubular macrophages in the rete testis were CX3CR1+F4/80+MHCIIhigh, but also expressed CD206, unlike peritubular macrophages in the seminiferous tubules. These data indicate that majority of macrophages within the rete testis and subcapsular regions are phenotypically different from macrophages in the rest of the parenchyma in that they have an activated, although anti-inflammatory, phenotype. Accumulation of these macrophages and the anti-inflammatory phenotype of the peritubular macrophages, within the rete testis suggest that they may play a role in recognising sperm antigens and providing protection for mature sperm in the absence of the blood-testis barrier. We predict that loss of the protective function of these macrophages during inflammatory disease may lead to sperm autoimmunity.